Insight into the evolutionary and domesticated history of the most widely cultivated mushroom Agaricus bisporus via mitogenome sequences of 361 global strains.

Agaricus bisporus is the most widely cultivated edible mushroom in the world with a only around three hundred years known history of cultivation. Therefore, it represents an ideal organism not only to investigate the natural evolutionary history but also the understanding on the evolution going back to the early era of domestication. In this study, we generated the mitochondrial genome sequences of 352 A. bisporus strains and 9 strains from 4 closely related species around the world. The population mitogenomic study revealed all A. bisporus strains can be divided into seven clades, and all domesticated cultivars present only in two of those clades. The molecular dating analysis showed this species origin in Europe on 4.6 Ma and we proposed the main dispersal routes. The detailed mitogenome structure studies showed that the insertion of the plasmid-derived dpo gene caused a long fragment (MIR) inversion, and the distributions of the fragments of dpo gene were strictly in correspondence with these seven clades. Our studies also showed A. bisporus population contains 30 intron distribution patterns (IDPs), while all cultivars contain only two IDPs, which clearly exhibit intron loss compared to the others. Either the loss occurred before or after domestication, that could suggest that the change facilitates their adaptation to the cultivated environment.

Metabolomics and transcriptomics unravel the mechanism of browning resistance in Agaricus bisporus.

Agaricus bisporus is widely consumed on the world market. The easy browning of mushroom surface is one of the most intuitive factors affecting consumer purchase. A certain cognition on browning mechanism has been made after years of research. At present, people slow down the browning of mushrooms mainly by improving preservation methods. In addition, breeding is also a reliable way. In the production practice, we have identified some browning-resistant varieties, and we selected a browning-resistant variety to compare with an ordinary variety to reveal the resistance mechanism. Using transcriptomics and metabolomics, the differences in gene expression and metabolite levels were revealed, respectively. The results showed that differentially expressed genes (DEGs) like AbPPO4, AbPPO3 and AbPPO2 were differently expressed and these DEGs were involved in many pathways related to browning. The expression of AbPPO expression play an important role in the browning of A. bisporus and multiple PPO family members are involved in the regulation of browning. However, the resistance to browning cannot be judged only by the expression level of AbPPOs. For metabolomics, most of the different metabolites were organic acids. These organic acids had a higher level in anti-browning (BT) than easy-browning varieties (BS), although the profile was very heterogeneous. On the contrary, the content of trehalose in BS was significantly higher than that in BT. Higher organic acids decreased pH and further inhibited PPO activity. In addition, the BS had a higher content of trehalose, which might play roles in maintaining PPO activity. The difference of browning resistance between BS and BT is mainly due to the differential regulation mechanism of PPO.

Association between the hydrogenase level and the occurrence of remote diffusion-weighted imaging lesions after spontaneous intracerebral hemorrhage.

To explore the influence of serum lactate dehydrogenase (LDH) level on remote diffusion-weighted imaging lesions (rDWILs) after spontaneous intracerebral hemorrhage (ICH). A consecutive cohort of 160 patients with spontaneous ICH who had brain MRI within 4 weeks of ICH onset were collected and analyzed retrospectively. rDWILs showed high signal on diffusion-weighted image (DWI) while low signal on apparent diffusion coefficient (ADC), and at least 20 mm away from the hemorrhage focus. The blood samples were obtained within 24 h after ICH onset from all patients. Lactate dehydrogenase (LDH) levels in blood were collected from serum biochemical tests. We use multivariate logistic regression analyses to investigate the association between serum LDH level and rDWILs after ICH. The average serum LDH level was 186.5 ± 35.6 U/L. And this level was higher in patients who presented rDWILs than in those without rDWILs. With the best cut-off value of 191 by using receiver operating characteristic (ROC) analysis, elevated LDH was associated with the presence of rDWILs independently (OR = 1.024, 95%CI = 1.011-1.037, P < 0.001) in the bivariate logistic regression analysis with adjustment for age, sex, previous ischemic stroke/TIA, smoker, SBP on admission, hematoma volume, and intraventricular hemorrhage (IVH). The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) of LDH ≥ 191 U/L for rDWILs were 70.4%, 72.2%, 33.9%, 94.2%, respectively. Our study suggests serum LDH level has a significant correlation with rDWILs after spontaneous ICH. Patients with higher serum LDH level in 24 h after ICH onset may be a useful predictor for rDWILs occurrence.

USP9X promotes the progression of hepatocellular carcinoma by regulating beta-catenin.

Hepatocellular carcinoma (HCC) is among the malignant tumors with highest mortality. The role of USP9X in the carcinogenesis of HCC has not yet been determined. In this study, USP9X was found significantly highly expressed in the intratumor tissues. Expression of intratumor USP9X was associated with tumor size and microvascular invasion while USP9X is independent risk factor of HCC disease-free survival and overall survival. In vitro studies revealed that knockdown of USP9X significantly inhibited the proliferation of HCC cells. Mechanically, USP9X promotes HCC cell proliferation by regulating the expression of beta-catenin. The results of the present study demonstrated that high expression of USP9X in intratumoral cells is associated with poor HCC prognosis, which may serve as a potential target for an adjuvant therapy.

Genome Survey and Transcriptome Analysis on Mycelia and Primordia of Agaricus blazei.

Agaricus blazei, a type of edible straw-rotting mushroom with somewhat sweet taste and fragrance of almonds, has attracted considerable scientific and practical attention. High-throughput Illumina PE150 and PacBio RSII platform were employed to generate a genomic sequence. De novo assembly generated 36 contigs with 38,686,133 bp in size, containing 10,119 putative predicted genes. Additionally, we also studied transcriptional regulation of the mycelia and the primordia for exploration of genes involved in fruiting body formation. Expression profiling analysis revealed that 2,164 genes were upregulated in mycelia and 1,557 in primordia. Functional enrichment showed that differentially expressed genes associated with response to stress, ribosome biogenesis, arginine biosynthesis, and steroid biosynthesis pathway were more active in fruiting body. The genome and transcriptome analysis of A. blazei provide valuable sequence resources and contribute to our understanding of genes related to the biosynthesis pathway of polysaccharide and benzaldehyde, as well as the fruiting body formation.

An Eight-CpG-based Methylation Classifier for Preoperative Discriminating Early and Advanced-Late Stage of Colorectal Cancer.

AIM: To develop and validate a CpG-based classifier for preoperative discrimination of early and advanced-late stage colorectal cancer (CRC). METHODS: We identified an epigenetic signature based on methylation status of multiple CpG sites (CpGs) from 372 subjects in The Cancer Genome Atlas (TCGA) CRC cohort, and an external cohort (GSE48684) with 64 subjects by LASSO regression algorithm. A classifier derived from the methylation signature was used to establish a multivariable logistic regression model to predict the advanced-late stage of CRC. A nomogram was further developed by incorporating the classifier and some independent clinical risk factors, and its performance was evaluated by discrimination and calibration analysis. The prognostic value of the classifier was determined by survival analysis. Furthermore, the diagnostic performance of several CpGs in the methylation signature was evaluated. RESULTS: The eight-CpG-based methylation signature discriminated early stage from advanced-late stage CRC, with a satisfactory AUC of more than 0.700 in both the training and validation sets. This methylation classifier was identified as an independent predictor for CRC staging. The nomogram showed favorable predictive power for preoperative staging, and the C-index reached 0.817 (95% CI: 0.753-0.881) and 0.817 (95% CI: 0.721-0.913) in another training set and validation set respectively, with good calibration. The patients stratified in the high-risk group by the methylation classifier had significantly worse survival outcome than those in the low-risk group. Combination diagnosis utilizing only four of the eight specific CpGs performed well, even in CRC patients with low CEA level or at early stage. CONCLUSIONS: Our classifier is a valuable predictive indicator that can supplement established methods for more accurate preoperative staging and also provides prognostic information for CRC patients. Besides, the combination of multiple CpGs has a high value in the diagnosis of CRC.

Depletion of STYK1 inhibits intrahepatic cholangiocarcinoma development both in vitro and in vivo.

Intrahepatic cholangiocarcinoma (ICC) has been reported to be the second most common primary hepatic carcinoma worldwide, and very limited therapies are currently available. Serine threonine tyrosine kinase (STYK1), a member of the receptor tyrosine kinase family, exhibits tumorigenicity in many types of cancers and is a potential therapeutic target for ICC. In this study, STYK1 was knocked down in the ICC cell lines HCCC-9810 and RBE via a lentivirus-mediated system using short hairpin RNA (shRNA). Next, cell proliferation, colony formation, cell cycle progression, tumor formation in nude mice, migration and invasion, and the expression levels of cell cycle proteins in Lv-sh STYK1- or Lv-sh Con-infected cells were analyzed by CCK-8 assay, colony formation evaluation, flow cytometry, tumor formation evaluation, wound scratch assay, transwell assay, and western blotting. The results indicated that depletion of STYK1 inhibits ICC development both in vitro and in vivo.

Tumor suppressor Fbxw7 antagonizes WNT signaling by targeting ß-catenin for degradation in pancreatic cancer.

Pancreatic cancer is one of the deadliest solid malignancies associated with aberrant Wnt signaling activation. Fbxw7 mutations have been implicated in the development of pancreatic cancer, whereas the exact mechanism of this ubiquitin ligase as a tumor suppressor remains unclear in pancreatic carcinogenesis. Here, we describe that Fbxw7 is downregulated upon pancreatic cancer development. Depletion of Fbxw7 results in tumor suppression in pancreatic cancer cells, while Fbxw7 overexpression inhibits pancreatic cancer cell proliferation and invasion. Considering the negative correlation between Fbxw7 and ß-catenin, we find that Fbxw7 antagonizes Wnt signaling through targeting ß-catenin for its degradation. Moreover, the inhibitory effect of Fbxw7 on pancreatic cancer cell proliferation is mainly executed by the destruction of the Wnt/ß-catenin signaling pathway. We also reveal that c-myc, a widely accepted target of Fbxw7, is also transcriptionally regulated by the Fbxw7/ß-catenin axis in pancreatic cancer cells. Collectively, our results demonstrate that Fbxw7 is a novel regulator of Wnt/ß-catenin signaling-dependent regulation of pancreatic cancer cell growth and invasion, and inactivation of Fbxw7 in pancreatic cancer tissues might be the reason for the aberrant activation of Wnt signaling.

Insights into significant pathways and gene interaction networks in peripheral blood mononuclear cells for early diagnosis of hepatocellular carcinoma.

BACKGROUND: Early diagnosis of hepatocellular cancer (HCC) significantly helps improve patient survival. However, high specific and sensitive tests for screening patients with early stage of HCC are not yet available. Novel HCC biomarkers based on gene expression profiles of peripheral blood mononuclear cells (PBMCs) might change the situation. Recently, a three gene-based signature for the non-invasive detection of early HCC was reported. OBJECTIVE: To compare the differences in global gene expression profiles in PBMCs of healthy individuals and HCC patients, with a specific aim to uncover the significantly altered biological pathways and important hub genes. MATERIALS AND METHODS: Two groups of data were extracted from Affymetrix microarray expression dataset GSE49515. One group had 10 PBMCs samples from healthy control individuals, and the other had 10 PBMCs samples from patients with HCC. Gene expression profiles of both groups were analyzed and compared. Furthermore, ribonucleic acid (RNA) levels of seven of the identified differentially expressed genes (DEGs) were further confirmed by quantitative reverse transcription polymerase chain reaction (QRT-PCR). RESULTS: Significant differences were uncovered in gene expression profiles in PBMCs of healthy individuals and HCC patients. Three hundred and seventy-five up-regulated and 169 down-regulated DEGs were identified. Three hundred and eighty-seven gene ontology (GO) biological processes and 15 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were over-represented by the identified DEGs. CONCLUSIONS: Using identified DEGs, significantly changed biological processes such as nucleic acid metabolic process and KEGG pathways such as cytokine-cytokine receptor interaction in PBMCs of HCC patients were identified. In addition, several important hub genes, for example, CUL4A, and interleukin (IL) 8 were also uncovered.

Expression and significance of HIF-1α and HIF-2α in pancreatic cancer.

The expression levels of hypoxia-inducible factor 1alpha (HIF-1α) and HIF-2α in pancreatic cancer (PC) and their association with clinicopathologic characteristics were investigated in order to elucidate their roles in the development of PC. HIF-1α and HIF-2α mRNA levels in 20 patients with PC were detected by quantitative real-time polymerase chain reaction. The expression of HIF-1α and HIF-2α protein in samples from other 90 patients with PC was measured by immunohistochemistry. Correlations between the expression of HIF-1α or HIF-2α and clinicopathologica features and prognosis were analyzed. The expression of both HIF-1α and HIF-2α mRNA was up-regulated in most cancer tissues (P<0.05). HIF-1α staining was weakly positive in most cancer tissues and strongly positive in adjacent pancreas tissues (P<0.05). Clinicopathologic analysis revealed that relatively strong HIF-1α expression in cancer tissues was related to greater invasion (P<0.05), higher tumor pathologic stage (P<0.05), higher American Joint Committee on Cancer (AJCC) stage (P<0.05) and shorter overall survival time (P<0.05). Conversely, HIF-2α staining was strongly positive in most cancer tissues and weakly positive in adjacent pancreas tissues. Clinicopathologic analysis revealed that relatively strong HIF-2α expression in cancer tissues was related to less invasion (P<0.05), lower tumor pathologic stage (P<0.05), lower AJCC stage (P<0.05) and longer overall survival time (P<0.05). Moreover, the HIF-1α(high)/HIF-2α(low) group showed a shorter survival time than the HIF-1α(low)/HIF-2α(high) group. In conclusion, although HIF-1α and HIF-2α mRNA expression patterns are the same, their protein expression patterns are significantly different and they play different roles in PC. Combined analysis of HIF-1α and HIF-2α expression might be useful to predict the prognosis of patients with PC.

[Ginsenoside Rg1 antagonizes ß-amyloid peptide-induced apoptosis in primarily cultured rat neurons via mitochondrial pathway].

OBJECTIVE: To assess the neuroprotective effects of ginsenoside Rg1 against ß-amyloid peptide (Aß(25-35))-induced apoptosis in primarily cultured rat cortical neurons. METHODS: Primarily cultured cortical neurons were obtained from embryonic (E18d) rat fetus and maintained in neurobasal medium for 7d. Primary neurons pretreated with 1 µmol/L, 10 µmol/L or 20 µmol/L Rg1 for 24 h were challenged with 10 µmol/L Aß(25-35) for 72 h. Morphological changes of neurons were evaluated; mitochondrial membrane potential (ΔΨm) was measured; with JC-1 staining and the expression of neural apoptosis-related proteins was detected by Western blot analysis. RESULTS: Exposure to Aß(25-35) for 72 h caused serious neural cell insults. A pretreatment with Rg1 significantly reduced Aß(25-35)induced cell death in a dose-dependent manner, with a maximal effect (-90%) obtained at 20 µmol/L. The JC-1 staining results demonstrated the loss of ΔΨm after Aß(25-35) treatment, while Rg1 maintained the normal level of ΔΨm. A series of mitochondrion-mediated apoptotic events happened after Aß(25-35) treatment, such as decrease of Bcl-2/Bax, release of cytochrome C and activation of caspase 9 and caspase 3, which were all blocked by Rg1 pretreatment. Both estrogen receptor (ER) antagonist ICI182, 780 and glucocorticoid receptor (GR) antagonist RU486 blocked the antiapoptotic effects of Rg1. CONCLUSION: Ginsenoside Rg1 protects primary cultured rat cortical neurons from Aß(25-35)-induced injury, which may be associated with mitochondrion-mediated antiapoptosis pathway.

[Red clover isoflavones inhibit the proliferation and promote the apoptosis of benign prostatic hyperplasia stromal cells].

OBJECTIVE: To evaluate the effects of red clover isoflavones on the proliferation and apoptosis of human benign prostatic hyperplasia (BPH) stromal cells. METHODS: We treated human prostate stromal cells with red clover isoflavones at the concentration of 12.5, 25, 50 and 100 microg/ml, and established a PBS blank control, a dimethyl sulphoxide (DMSO) negative control and four finasteride positive control groups (at the concentration of 12.5, 25.0, 50.0 and 100.0 microg/ml). We determined the effects of different concentrations of red clover isoflavones on the proliferation of the cells by MTT assay and on their apoptosis by Annexin V/PI double staining flow cytometry. RESULTS: Red clover isoflavones inhibited the proliferation of the BPH stromal cells by 18.86% at 25.0 microg/ml, compared with 5.17% in the blank control group (P < 0.05), and more obviously at a higher concentration. At 50.0 microg/ml, red clover isoflavones exhibited a weaker inhibitory effect than finasteride (28% vs 69.88% , P < 0.05). Annexin V/PI double staining flow cytometry showed that red clover isoflavones at 25.0 microg/ml induced the apoptosis of the prostate stromal cells by (18.54 +/- 2.5)%, with significant differences from the negative control and blank control (P < 0.01). CONCLUSION: Red clover isoflavones can inhibit the proliferation and promote the apoptosis of human BPH stromal cells.